Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

Structural impact of a new spike Y170W mutation detected in early emerging SARS-CoV-2 Omicron variants in France

To assess the genetic characteristics of the early emerging SARS-CoV-2 Omicron variant strains, we retrospectively analyzed a collection of 150 nasopharyngeal samples taken from a series of outpatient cases tested positive by a referenced qRT-PCR assay during the reported period of Omicron variant emergence in December 2021, in northeastern region of France. Next Generation Sequencing (NGS) analysis of SARS-CoV-2 spike sequences revealed that only 3 (2 %) of these detected strains were Omicron variants, while 147 (98 %) were identified as previously described delta variants. Our phylogenetic analyzes of SARS-CoV-2 RNA genomes showed that these French early emerging Omicron variants may have originated from South Africa or India. In addition, whole viral genome sequences NGS comparison analyzes allowed us to identify an original and uncharacterized Y170W spike mutation that was weakly and transiently detected during the period of SARS-CoV-2 Omicron variant emergence in human populations. Molecular modeling and docking experiments indicated that this original mutated residue Y170W was neither directly involved in binding to the SARS-CoV-2 receptor ACE2 nor in interacting with known neutralizing antibody sites. However, this new mutation may be responsible for preventing the transition from the closed to the open Spike conformation, thus promoting the early emergence of the Omicron variant. Overall, these results underscore the epidemiological utility of a routine whole-genome viral NGS strategy that enables genotypic characterization of emerging or mutant SARS-CoV-2 variants, which could have significant implications for public health policy.

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

Targeting EGFR and VEGFR-2 Kinases With Nanoparticles: A Computational Approach for Cancer Therapy Advancement

The study investigates titanium and zinc nanoparticles as inhibitors for the epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor-2 (VEGFR-2), pivotal regulators of cell processes. VEGFR-2 activation fuels tumor angiogenesis in cancer cells, sustaining malignant tissue expansion. Molecular docking analysis illustrates the nanoparticles' binding to the active sites, inhibiting the phosphorylation of key proteins in downstream signaling. This inhibition offers a promising therapeutic approach to impede cancer-related signaling, potentially slowing down aberrant protein cascades controlled by EGFR and VEGFR-2. The findings propose a novel avenue for cancer treatment, targeting abnormal growth pathways using titanium and zinc nanoparticles.

Structural and functional validation of a cloned parasporin from Bacillus thuringiensis isolate KAU 41 native to Western Ghats of India

Parasporins of Bacillus thuringiensis (Bt) exhibit specific toxicity to cancer cells. PCR based mining has identified apoptosis inducing parasporin in KAU41 Bt isolate from the Western Ghats of India. The study aimed to clone and overexpress the parasporin of native KAU41 Bt isolate for determining structural and functional characteristics of the protein. Parasporin gene was cloned in pGEM-T, sequenced, sub-cloned in pET30+ and overexpressed in Escherichia coli. The expressed protein was characterized by SDS-PAGE and in silico methods. Cytotoxicity of cleaved peptide was assessed by MTT assay. SDS-PAGE displayed a 31 kDa protein (rp-KAU41) overexpressed. Upon proteinase K digestion, the protein was cleaved into 29 kDa peptide which was found to be cytotoxic to HeLa cells. The protein has a deduced sequence of 267 amino acids with β-strands folding pattern of crystal protein. Even though rp-KAU41 shared a 99.15% identity to chain-A of non-toxic crystal protein, it only showed a less similarity to the existing parasporins like PS4 (38%) and PS5 (24%) in UPGMA analysis, emphasizing the novelty of rp-KAU41. The protein is predicted to have more similarity to the pore forming toxins of Aerolysin superfamily and an additional loop in rp-KAU41 may be contributing towards its cytotoxicity. The molecular docking with caspase 3 resulted in higher Z dock and Z rank score substantiating its role in the activation of intrinsic pathway of apoptosis. The recombinant parasporin protein, rp-KAU41 is presumed to belong to the Aerolysin superfamily. An interaction with caspase 3 substantiates its role in activating the intrinsic pathway of apoptosis in cancer cells.

"Redirecting an anti-IL-1β antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A"

Antibody engineering technology is at the forefront of therapeutic antibody development. The primary goal for engineering a therapeutic antibody is the generation of an antibody with a desired specificity, affinity, function, and developability profile. Mature antibodies are considered antigen specific, which may preclude their use as a starting point for antibody engineering. Here, we explore the plasticity of mature antibodies by engineering novel specificity and function to a pre-selected antibody template. Using a small, focused library, we engineered AAL160, an anti-IL-1β antibody, to bind the unrelated antigen IL-17A, with the introduction of seven mutations. The final redesigned antibody, 11.003, retains favorable biophysical properties, binds IL-17A with sub-nanomolar affinity, inhibits IL-17A binding to its cognate receptor and is functional in a cell-based assay. The epitope of the engineered antibody can be computationally predicted based on the sequence of the template antibody, as is confirmed by the crystal structure of the 11.003/IL-17A complex. The structures of the 11.003/IL-17A and the AAL160/IL-1β complexes highlight the contribution of germline residues to the paratopes of both the template and re-designed antibody. This case study suggests that the inherent plasticity of antibodies allows for re-engineering of mature antibodies to new targets, while maintaining desirable developability profiles.

The Amphiphilic Property and Structure of β-Amyloid Peptide Contribute to Its Impacts on the Activities of Horseradish Peroxidase and Alkaline Phosphatase

Recent studies have found that β-amyloid (Aβ) oligomers may play much more important roles than amyloid plaques in the pathogenesis of Alzheimer's disease (AD). However, due to the complexity of Aβ, studying the structural basis of Aβ oligomer toxicity is challenging. Here, we assessed the amphiphilic property and β-hairpin structure of Aβ monomer. The potential impacts of Aβ oligomers and three sequence-modifying peptides on the enzyme activities of horseradish peroxidase (HRP) and alkaline phosphatase (ALP) were further evaluated. We demonstrated that Aβ oligomer possesses the ability to alter the activity of two enzymes. Moreover, modifications on the hydrophobic region and β-turn structure of Aβ monomer significantly alter its impacts on the enzyme activities. In addition, these modifications also change the bonding modes of Aβ monomers or oligomers binding to HRP, as assessed by molecular docking. All of these findings provide direct experimental evidence to reveal the critical roles of the amphiphilic property and β-sheet structure of Aβ monomer in its impacts on protein activity.

Modeling Protein Complexes and Molecular Assemblies Using Computational Methods

Many biological molecules are assembled into supramolecular complexes that are necessary to perform functions in the cell. Better understanding and characterization of these molecular assemblies are thus essential to further elucidate molecular mechanisms and key protein-protein interactions that could be targeted to modulate the protein binding affinity or develop new binders. Experimental access to structural information on these supramolecular assemblies is often hampered by the size of these systems that make their recombinant production and characterization rather difficult. Computational methods combining both structural data, molecular modeling techniques, and sequence coevolution information can thus offer a good alternative to gain access to the structural organization of protein complexes and assemblies. Herein, we present some computational methods to predict structural models of the protein partners, to search for interacting regions using coevolution information, and to build molecular assemblies. The approach is exemplified using a case study to model the succinate-quinone oxidoreductase heterocomplex.

Methanol extract of Black soldier fly (Hermetia illucens) prepupae against Aeromonas and Staphylococcus aureus bacteria in vitro and in silico

Background

Staphylococcus and Aeromonas bacteria are pathogens in humans and animals. The therapy disrupts the virulence structure of the bacteria, resulting in bacterial death. Currently, chemical drugs have resulted in many resistant bacteria, so it is necessary to find alternative natural materials that are not toxic and do not quickly induce resistance.

Aims

This study aimed to analyze the potential of methanol extract from Black soldier fly (BSF) prepupae as an antibacterial agent against Staphylococcus aureus and Aeromonas through in silico and in vitro tests.

Methods

The BSF prepupae methanol extract was analyzed for protein and fatty acid contents. Disc diffusion method, minimal inhibitory concentration, and minimum bactericidal concentration test were used for in vitro tests against Staphylococcis and Aeromonas. Molecular docking of the active ingredients (defensin, chitin, and chitosan as well as fatty acids) in BSF was downloaded from the NCBI database and docked by the Hex Cuda version 8.0 program with Correlation type parameters Shape + Electro and Grid Dimension version 0.6. Docking results were analyzed using the Discovery Studio program version 21.1.1.

Results

The highest fatty acid contents in the extract were palmitic acid and myristic acid. Methanol extract from BSF prepupae acted as a bactericidal agent against S. aureus at a concentration of 320 mg/ml, in contrast to Aeromonas, which still showed bacterial growth. The results of the in silico test showed that defensin-aerolysin and defensin-hemolysin was bound to the same active site area. However, the amount of binding energy produced by 69-Defensin-83-aerolysin was higher than all defensin types in BSF against Aeromonas. Chitin and chitosan showed a bond on the active site of aerolysin and hemolysin, but chitosan had a stronger bond than chitin. In silico study also showed the strongest binding affinity of BSF fatty acids to isoleucyl-tRNA synthetase of S. aureus.

Conclusion

The study showed that methanol extract from BSF prepupae had potential capability as an antibacterial agent against S. aureus than Aeromonas in vitro and in silico.

Polydopamine nanospheres coated with bovine serum albumin permit enhanced cell differentiation: fundamental mechanism and practical application for protein coating formation

Protein coating is a strategy for modifying and improving the surface functional properties of nanomaterials. However, the underlying mechanism behind protein coating formation, which is essential for its practical applications, remains largely unknown. Herein, we investigate the fundamental molecular mechanism of protein coating formation. Polydopamine nanospheres (PDANS) coated with bovine serum albumin (BSA) are examined in this study due to their wide biomedical potential. Our results demonstrate that BSAs can flexibly bind to PDANS and maintain their structural dynamicity. Our findings unveil that regular structure formation arises from BSAs lateral interactions via electrostatic forces. Notably, the protein coating modified PDANS surface enhances cell adhesion and proliferation as well as osteogenic differentiation. Such an enhancement is attributed to complementary surface properties provided by the dynamic PDANS-BSA complex and regular structure caused by BSA-BSA interactions in protein coating formation. This study provides a fundamental understanding of the molecular mechanism of protein coating formation, which facilitates the further development of functional protein-coated nanomaterials and guides the bioengineering decision making for biomedical applications, especially in bone tissue engineering.

Differential MMP-14 Targeting by Lumican-Derived Peptides Unraveled by In Silico Approach

Lumican, a small leucine-rich proteoglycan (SLRP) of the extracellular matrix (ECM), displays anti-tumor properties through its direct interaction with MMP-14. Lumican-derived peptides, such as lumcorin (17 amino acids) or L9M (10 amino acids), are able to inhibit the proteolytic activity of MMP-14 and melanoma progression. This work aimed to visualize the interactions of lumican-derived peptides and MMP-14. Molecular modeling was used to characterize the interactions between lumican-derived peptides, such as lumcorin, L9M, and cyclic L9M (L9Mc, 12 amino acids), and MMP-14. The interaction of L9Mc with MMP-14 was preferential with the MT-Loop domain while lumcorin interacted more with the catalytic site. Key residues in the MMP-14 amino acid sequence were highlighted for the interaction between the inhibitory SLRP-derived peptides and MMP-14. In order to validate the in silico data, MMP-14 activity and migration assays were performed using murine B16F1 and human HT-144 melanoma cells. In contrast to the HT-144 melanoma cell line, L9Mc significantly inhibited the migration of B16F1 cells and the activity of MMP-14 but with less efficacy than lumican and lumcorin. L9Mc significantly inhibited the proliferation of B16F1 but not of HT-144 cells in vitro and primary melanoma tumor growth in vivo. Thus, the site of interaction between the domains of MMP-14 and lumcorin or L9Mc were different, which might explain the differences in the inhibitory effect of MMP-14 activity. Altogether, the biological assays validated the prediction of the in silico study. Possible and feasible improvements include molecular dynamics results.

ZEAL: protein structure alignment based on shape similarity

MOTIVATION

Most protein-structure superimposition tools consider only Cartesian coordinates. Yet, much of biology happens on the surface of proteins, which is why proteins with shared ancestry and similar function often have comparable surface shapes. Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites.

RESULTS

We present ZEAL, an interactive tool to superpose global and local protein structures based on their shape resemblance using 3D (Zernike-Canterakis) functions to represent the molecular surface. In a benchmark study of structures with the same fold, we show that ZEAL outperforms two other methods for shape-based superposition. In addition, alignments from ZEAL were of comparable quality to the coordinate-based superpositions provided by TM-align. For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. In combination with shape-based matching, ZEAL can be used as a general tool to study relationships between shape and protein function. We identify several categories of protein functions where global shape similarity is significantly more likely than expected by random chance, when comparing proteins with little similarity on the fold level. In particular, we find that global surface shape similarity is particular common among DNA binding proteins.

AVAILABILITY AND IMPLEMENTATION

ZEAL can be used online at https://andrelab.org/zeal or as a standalone program with command line or graphical user interface. Source files and installers are available at https://github.com/Andre-lab/ZEAL.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Exploring effectiveness of ab-initio protein-protein docking methods on a novel antibacterial protein complex dataset

Diseases caused by bacterial infections become a critical problem in public heath. Antibiotic, the traditional treatment, gradually loses their effectiveness due to the resistance. Meanwhile, antibacterial proteins attract more attention because of broad spectrum and little harm to host cells. Therefore, exploring new effective antibacterial proteins is urgent and necessary. In this paper, we are committed to evaluating the effectiveness of ab-initio docking methods in antibacterial protein-protein docking. For this purpose, we constructed a three-dimensional (3D) structure dataset of antibacterial protein complex, called APCset, which contained $19$ protein complexes whose receptors or ligands are homologous to antibacterial peptides from Antimicrobial Peptide Database. Then we selected five representative ab-initio protein-protein docking tools including ZDOCK3.0.2, FRODOCK3.0, ATTRACT, PatchDock and Rosetta to identify these complexes' structure, whose performance differences were obtained by analyzing from five aspects, including top/best pose, first hit, success rate, average hit count and running time. Finally, according to different requirements, we assessed and recommended relatively efficient protein-protein docking tools. In terms of computational efficiency and performance, ZDOCK was more suitable as preferred computational tool, with average running time of $6.144$ minutes, average Fnat of best pose of $0.953$ and average rank of best pose of $4.158$. Meanwhile, ZDOCK still yielded better performance on Benchmark 5.0, which proved ZDOCK was effective in performing docking on large-scale dataset. Our survey can offer insights into the research on the treatment of bacterial infections by utilizing the appropriate docking methods.

Top Down Computational Approach: A Vaccine Development Step to Find Novel Superantigenic HLA Binding Epitopes from Dengue Virus Proteome

Dengue virus (DENV) is a major mosquito vector based human pathogenic flavivirus which is causing major threat worldwide, yet the availability of therapeutic treatment and several vaccines, still called for advance treatment and vaccine development. The present top down computational approach is a vaccine development step to find novel super antigenic HLA binding epitopes from DENV proteome. The approach used sequence based screening to find complete conserve and high population coverage, common epitopes among all DENV serotype. Propred and Immune Epitope Data Base were used for sequence based screening with recommended parameters. Among top 29 identified epitopes, five structural protein epitopes viz. ³³LQGRGPLKL⁴¹, ²⁴⁹VVVLGSQEG²⁵⁷, ¹⁷²LVGIVTLYL¹⁸⁰, ¹⁴⁶MKILIGVVI¹⁵⁴, ⁷²YIIVGVEPG⁸⁰ and one nonstructural protein epitope ¹⁸LKNDIPMTG²⁶ were showed high conserve nature and high population coverage from complete DENV proteome. Further structure based study involving docking and molecular dynamic simulation to confirm stable behavior of HLA allele–peptide complex to give potent cell mediated immune response. Docking of epitope ⁷²YIIVGVEPG⁸⁰–DRB1 0401 allele and epitope ³³LQGRGPLKL⁴¹–B*5101 allele complexes showed the best binding energy of − 7.71 and − 7.20 kcal/mol, respectively and stable binding pattern over the time window during molecular dynamic simulation. This computational approach resulted novel epitopes which can be used in the design and development of short epitope based vaccines as well as diagnosis tools for dengue infection.

In silico-based Approach to Investigate the Ability of PEGylated Rapamycin to Inhibit Galectin-3

AIMS

To utilize in silico-based approach for investigating the ability of PEGylated rapamycin as a competitive inhibitor to Galectin-3 for curing various diseases or that may provide an attractive strategy for treatment of a wide variety of tumors.

BACKGROUND

Galectin-3 (Gal-3) signaling protein is a unique member of lectin family present at the cell surface, intracellularly in both the nucleus and cytoplasm and extracellularly in the general circulation. Circulating Gal-3 is present in both normal and cancer cells. High levels of circulating Gal-3 have been proven to be associated with inflammation and fibrosis in several acute and chronic conditions, which include neurological degeneration, inflammatory and immune responses, autoimmune diseases, diabetes, heart failure, atherosclerosis, response to infection, wound healing, liver, lung, and kidney disease. Gal-3 is known to regulate many biological activities including cell adhesion, angiogenesis, growth, apoptosis, migration, and metastasis. Rapamycin has been examined alone or in combination with other drugs for treatment of various cancers in clinical studies. Although it has shown promising therapeutic effects, its clinical development was interrupted by poor aqueous solubility and limited preferential distribution. To overcome these limitations, RA has been chemically modified to hydrophilic analogues, such as everolimus (EV). However, all these approaches can only partially increase the solubility, but has little effect on the blood distribution and pharmacokinetics. Therefore, it is necessary to explore other RA conjugates to improve aqueous solubility and tissue distribution profile. Recently we reported that RP-MPEG inhibits the growth of various cancer cell lines by acting on mammalian target of RP (mTOR) receptor site and it can be used for gastric cancer.

OBJECTIVE

To construct various molecular weight RP-MPEG by replacing MPEG chain in 40-O-(2- hydroxyethyl) position of the EV and analyze their binding affinity to Gal-3.

METHODS

The chemical structures of various molecular weight RP-MPEG were built using ChemSketch software. The molecular docking study was performed to find the best probable structure of RP-MPEG for competitive inhibition of the CRD, based on the interaction score. For that purpose, the 3D structures of RP and EV were obtained from NCBI PubChem compound database, where the structural protein-co-crystallized ligand complex of Gal-3 (TD2, as a native ligand) was retrieved from RCSB Protein Data Bank. All structures of the selected compounds, served as molecules for molecular modeling, were optimized through MOE.2014 software before docking. Hydrogen atoms and partial charges were added to the protein. Protein minimization was performed in gas solvation with the side chains, keeping it rigid and the ligand flexible. The selected site was isolated and minimized, followed by protonating the protein. The 3D ligands were minimized using MMFF94x with cutoffs of 10 to 12 Å. The hydrogens and charges were fixed, and the RMS gradient was set to 0.001 kcal/mol. The docking results were analyzed to identify and assess the binding affinity of these compounds to CRD using drug discovery software.

RESULTS

Our results indicated that RP-MPEG with MW 1178.51 g/mol has a logP value of 3.79 and has possessed the strongest binding affinity toward CRD of Gal-3 with a docking score of -6.87. Compared with TD2, there were additional close contacts for RP-MPEG (MW 1178.51 g/mol), coming from three hydrogen bonds with Asp148, Arg162, and Arg144 which suggest that this ligand is a strong competitive inhibitor among the other molecules for Gal-3.

CONCLUSION

RP-MPEG with the MW 1178.51 g/mol could be a promising blocker for various biological action of Gal-3 includes profibrotic activity, modulation of immune responses and inflammatory responses to cancer that contributes to neoplastic transformation, angiogenesis and metastasis. Other: The 95% confidence intervals (CIs) of the binding affinity (according to their mean and standard errors) were estimated with 2.5 and 97.5 percentile as the lower and upper bounds.

Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription

OBJECTIVE

The HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin.

DESIGN

We explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA (lncRNA) expressed in the liver and increased in human hepatocellular carcinoma (HCC), in the regulation of host target genes and the HBV cccDNA.

RESULTS

We show that HBx binds the promoter region, enhances the transcription and induces the accumulation of DLEU2 in infected hepatocytes. We found that nuclear DLEU2 directly binds HBx and the histone methyltransferase enhancer of zeste homolog 2 (EZH2), the catalytic active subunit of the polycomb repressor complex 2 (PRC2) complex. Computational modelling and biochemical evidence suggest that HBx and EZH2 share two preferential binding sites in DLEU2 intron 1. HBx and DLEU2 co-recruitment on the cccDNA displaces EZH2 from the viral chromatin to boost transcription and viral replication. DLEU2-HBx association with target host promoters relieves EZH2 repression and leads to the transcriptional activation of a subset of EZH2/PRC2 target genes in HBV-infected cells and HBV-related HCCs.

CONCLUSIONS

Our results highlight the ability of HBx to bind RNA to impact on the epigenetic control of both viral cccDNA and host genes and provide a new key to understand the role of DLEU2 and EZH2 overexpression in HBV-related HCCs and HBx contribution to hepatocytes transformation.

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction

MOTIVATION

Template-based and template-free methods have both been widely used in predicting the structures of protein-protein complexes. Template-based modeling is effective when a reliable template is available, while template-free methods are required for predicting the binding modes or interfaces that have not been previously observed. Our goal is to combine the two methods to improve computational protein-protein complex structure prediction.

RESULTS

Here, we present a method to identify and combine high-confidence predictions of a template-based method (SPRING) with a template-free method (ZDOCK). Cross-validated using the protein-protein docking benchmark version 5.0, our method (ZING) achieved a success rate of 68.2%, outperforming SPRING and ZDOCK, with success rates of 52.1% and 35.9% respectively, when the top 10 predictions were considered per test case. In conclusion, a statistics-based method that evaluates and integrates predictions from template-based and template-free methods is more successful than either method independently.

AVAILABILITY AND IMPLEMENTATION

ZING is available for download as a Github repository (https://github.com/weng-lab/ZING.git).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Tumor markers as an entry for SARS-CoV-2 infection?

Coronavirus disease 2019 (COVID‐19), the highly contagious illness caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has spread across the globe, becoming one of the most challenging public health crisis of our times. SARS‐CoV‐2 can cause severe disease associated with multiple organ damage. Cancer patients have a higher risk of SARS‐CoV‐2 infection and death. While the virus uses angiotensin‐converting enzyme 2 (ACE2) as the primary entry receptor, the recent experimental and clinical findings suggest that some tumor markers, including CD147 (basigin), can provide an additional entry for SARS‐CoV‐2 infection through binding to the viral spike (S) protein. In the absence of specific viral drugs, blocking of CD147 might be a way to prevent virus invasion. Identifying other target proteins is of high importance as targeting the alternative receptors for SARS‐CoV‐2 might open up a promising avenue for the treatment of COVID‐19 patients, including those who have cancer.

In-vitro interaction of cerium oxide nanoparticles with hemoglobin, insulin, and dsDNA at 310.15 K: Physicochemical, spectroscopic and in-silico study

Lanthanide nanoparticles and nanorods especially their biocompatible oxide forms like cerium oxide nanoparticles (CNPs) with therapeutic applications are used to cure neurological oxidative stresses. Thus it tempts to study their biocompatible aspects by interactions with several biologically significant molecules. In-Vitro interactions of 15-240 μM CNPs with water, Phosphate buffered saline (PBS), DMEM media, Insulin (Ins) hemoglobin (Hb) and ds-DNA at 37 °C were studied. Their physicochemical properties study by Borosil Mansingh Survismeter (BMS) showed the first order interaction with the protein-protein structure breaking behaviour of CNPs with Hb, Ins, and DNA. Zeta potential measurements of CNPs in different biological medium show a net increase in negative charge magnitude with good colloidal stability. K_b = 4 × 106 mM^-1 of CNPs-DNA infer noncovalent interactions. Circular dichroism and FTIR revealed a loss of secondary conformation with increasing CNPs concentration. In-silico molecular docking depicts CNP interaction via conventional hydrogen bonding, carbon hydrogen bonding and electrostatic interactions at the minor groove of DNA. The study reports in-dept unfolding functional mechanism investigated by physicochemical, spectroscopic, and In-Silico approaches of protein on interactions with CNPs for safer-by-design use in medicine and pharmaceutics. Fundamentally the CeO₂ in ~62% and Ce₂O₃ in ~38% with Ce⁴⁺ and Ce³⁺ oxidation potentials develop a unique case of electronic configurations with 4f⁰5d⁰6s⁰ and 4f¹5d⁰6s⁰ electrons respectively which these studies a novel one.

Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms

Fast Fourier transform (FFT)-based protein ligand docking together with parallel simulated annealing for both rigid and flexible receptor docking are implemented on graphical processing unit (GPU) accelerated platforms to significantly enhance the throughput of the CDOCKER and flexible CDOCKER - the docking algorithms in the CHARMM program for biomolecule modeling. The FFT-based approach for docking, first applied in protein-protein docking to efficiently search for the binding position and orientation of proteins, is adapted here to search ligand translational and rotational spaces given a ligand conformation in protein-ligand docking. Running on GPUs, our implementation of FFT docking in CDOCKER achieves a 15 000 fold speedup in the ligand translational and rotational space search in protein-ligand docking problems. With this significant speedup it becomes practical to exhaustively search ligand translational and rotational space when docking a rigid ligand into a protein receptor. We demonstrate in this paper that this provides an efficient way to calculate an upper bound for docking accuracy in the assessment of scoring functions for protein-ligand docking, which can be useful for improving scoring functions. The parallel molecular dynamics (MD) simulated annealing, also running on GPUs, aims to accelerate the search algorithm in CDOCKER by running MD simulated annealing in parallel on GPUs. When utilized as part of the general CDOCKER docking protocol, acceleration in excess of 20 times is achieved. With this acceleration, we demonstrate that the performance of CDOCKER for redocking is significantly improved compared with three other popular protein-ligand docking programs on two widely used protein ligand complex data sets: the Astex diverse set and the SB2012 test set. The flexible CDOCKER is similarly improved by the parallel MD simulated annealing on GPUs. Based on the results presented here, we suggest that the accelerated CDOCKER platform provides a highly competitive docking engine for both rigid-receptor and flexible-receptor docking studies and will further facilitate continued improvement in the physics-based scoring function employed in CDOCKER docking studies.

Computational target-based drug repurposing of elbasvir, an antiviral drug predicted to bind multiple SARS-CoV-2 proteins

Coronavirus disease 19 (COVID-19) is a severe acute respiratory syndrome caused by SARS-CoV-2 (2019-nCoV). While no drugs have yet been approved to treat this disease, small molecules effective against other viral infections are under clinical evaluation for therapeutic abatement of SARS-CoV-2 infections. Ongoing clinical trials include Kaletra (a combination of two protease inhibitors approved for HIV treatment), remdesivir (an investigational drug targeting RNA-dependent RNA polymerase [RdRP] of SARS-CoV-2), and hydroxychloroquine (an approved anti-malarial and immuno-modulatory drug). Since SARS-CoV-2 replication depends on three virally encoded proteins (RdRP, papain-like proteinase, and helicase), we screened 54 FDA-approved antiviral drugs and ~3300 investigational drugs for binding to these proteins using targeted and unbiased docking simulations and computational modeling. Elbasvir, a drug approved for treating hepatitis C, is predicted to bind stably and preferentially to all three proteins. At the therapeutic dosage, elbasvir has low toxicity (liver enzymes transiently elevated in 1% of subjects) and well-characterized drug-drug interactions. We predict that treatment with elbasvir, alone or in combination with other drugs such as grazoprevir, could efficiently block SARS-CoV-2 replication. The concerted action of elbasvir on at least three targets essential for viral replication renders viral mutation to drug resistance extremely unlikely.

Anti-gastric cancer activity of 1,2,3-triazolo[4,5-d]pyrimidine hybrids (1,2,3-TPH): QSAR and molecular docking approaches

Gastric cancer as a dreaded disease which occurs in the digestive system of human being remain a threat to the medical world. Bioactivity of series of designed and synthesized molecular compounds containing triazole and pyrimidine moieties were subjected to quantum chemical calculations using B3LYP/6-31+G∗. The calculated molecular descriptors such as the EHOMO (eV), ELUMO (eV), band gap (eV), chemical hardness (η), global nucleophilicity, dipole moment (Debye), chemical potential, log P, molecular weight (amu) and Ovality. The descriptors that describe anti-gastric cancer activity of the studied compounds were used for QSAR analysis using SPSS and Gretl software packages for multiple linear regression (MLR), XLSTAT for partial least square (PLS) and MATLAB for artificial neural network (ANN). The methods (MLR, PLS, and ANN) were predictive. Nevertheless, ANN performed better than MLR and PLS. More so, molecular docking study was executed on the studied compounds and gastric cancer cell line (PDB ID:4oum); the docking studies showed that 2-(1-(2-(3-benzyl-5-(benzylthio)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-7-yl)hydrazono)ethyl)phenol (A22) having the lowest binding affinity (-8.40 kcal/mol); this was correlated to the observed inhibitory activity of the compound against gastric cancer. Thus, it showed better inhibition than other studied compounds. The amino acid residues that were involved in stabilizing A22 in the active site of the 4oum are: VAL-9, ALA-10, THR-49, ASN-48, PRO-47 and TYR-46. Also, a good relationship was observed between the calculated binding affinity and the observed inhibition concentration (IC50).

Fluoroquinolone antibiotics show genotoxic effect through DNA-binding and oxidative damage

The fluoroquinolones (FQs) are one the most successful class of synthetic antibiotics that primarily target the type II topoisomerases. With a pursuit to evaluate their genotoxicity, the present work established moderate to good DNA-damaging properties of some of the well-known and clinically prescribed fluoroquinolone antibiotics (2^nd and 3^rd generation). Hypochromic shift in UV-Vis absorption titration, fluorescence quenching in competitive ethidium bromide displacement assay (with calf-thymus DNA) and in-silico studies established DNA-intercalation with binding constants of the order 10⁴. A basic Structure Activity Relationship (SAR) has been derived from the docking results. MTT assay has been also done to evaluate the effect of these antibiotics on cell viability. The expression level of specific DNA-glycosylase enzymes responsible for repairing the oxidized DNA bases are quantified through western blot analysis. The studies revealed that fluoroquinolone antibiotics initiate the genotoxic effect at a concentration of above 50 μg/mL. Recruitment of APE1 and NEIL1 was found to be significantly increased to remove the oxidized nucleobases.

EC313-a tissue selective SPRM reduces the growth and proliferation of uterine fibroids in a human uterine fibroid tissue xenograft model

Uterine fibroids (UFs) are associated with irregular or excessive uterine bleeding, pelvic pain or pressure, or infertility. Ovarian steroid hormones support the growth and maintenance of UFs. Ulipristal acetate (UPA) a selective progesterone receptor (PR) modulator (SPRM) reduce the size of UFs, inhibit ovulation and lead to amenorrhea. Recent liver toxicity concerns with UPA, diminished enthusiasm for its use and reinstate the critical need for a safe, efficacious SPRM to treat UFs. In the current study, we evaluated the efficacy of new SPRM, EC313, for the treatment for UFs using a NOD-SCID mouse model. EC313 treatment resulted in a dose-dependent reduction in the fibroid xenograft weight (p < 0.01). Estradiol (E2) induced proliferation was blocked significantly in EC313-treated xenograft fibroids (p < 0.0001). Uterine weight was reduced by EC313 treatment compared to UPA treatment. ER and PR were reduced in EC313-treated groups compared to controls (p < 0.001) and UPA treatments (p < 0.01). UF specific desmin and collagen were markedly reduced with EC313 treatment. The partial PR agonism and no signs of unopposed estrogenicity makes EC313 a candidate for the long-term treatment for UFs. Docking studies have provided a structure based explanation for the SPRM activity of EC313.

In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts

Tetherin, an interferon-induced host protein encoded by the bone marrow stromal antigen 2 (BST2/CD317/HM1.24) gene, is involved in obstructing the release of many retroviruses and other enveloped viruses by cross-linking the budding virus particles to the cell surface. This activity is antagonized in the case of human immunodeficiency virus (HIV)-1 wherein its accessory protein Viral Protein U (Vpu) interacts with tetherin, causing its downregulation from the cell surface. Vpu and tetherin connect through their transmembrane (TM) domains, culminating into events leading to tetherin degradation by recruitment of β-TrCP2. However, mutations in the TM domains of both proteins are reported to act as a resistance mechanism to Vpu countermeasure impacting tetherin's sensitivity towards Vpu but retaining its antiviral activity. Our study illustrates the binding aspects of blood-derived, brain-derived, and consensus HIV-1 Vpu with tetherin through protein-protein docking. The analysis of the bound complexes confirms the blood-derived Vpu-tetherin complex to have the best binding affinity as compared to other two. The mutations in tetherin and Vpu are devised computationally and are subjected to protein-protein interactions. The complexes are tested for their binding affinities, residue connections, hydrophobic forces, and, finally, the effect of mutation on their interactions. The single point mutations in tetherin at positions L23Y, L24T, and P40T, and triple mutations at {L22S, F44Y, L37I} and {L23T, L37T, T45I}, while single point mutations in Vpu at positions A19H and W23Y and triplet of mutations at {V10K, A11L, A19T}, {V14T, I18T, I26S}, and {A11T, V14L, A15T} have revealed no polar contacts with minimal hydrophobic interactions between Vpu and tetherin, resulting in reduced binding affinity. Additionally, we have explored the aggregation potential of tetherin and its association with the brain-derived Vpu protein. This work is a possible step toward an understanding of Vpu-tetherin interactions.

A genetically encoded fluorescent temperature sensor derived from the photoactive Orange Carotenoid Protein

The heterogeneity of metabolic reactions leads to a non-uniform distribution of temperature in different parts of the living cell. The demand to study normal functioning and pathological abnormalities of cellular processes requires the development of new visualization methods. Previously, we have shown that the 35-kDa photoswitchable Orange Carotenoid Protein (OCP) has a strong temperature dependency of photoconversion rates, and its tertiary structure undergoes significant structural rearrangements upon photoactivation, which makes this protein a nano-sized temperature sensor. However, the determination of OCP conversion rates requires measurements of carotenoid absorption, which is not suitable for microscopy. In order to solve this problem, we fused green and red fluorescent proteins (TagGFP and TagRFP) to the structure of OCP, producing photoactive chimeras. In such chimeras, electronic excitation of the fluorescent protein is effectively quenched by the carotenoid in OCP. Photoactivation of OCP-based chimeras triggers rearrangements of complex geometry, permitting measurements of the conversion rates by monitoring changes of fluorescence intensity. This approach allowed us to determine the local temperature of the microenvironment. Future directions to improve the OCP-based sensor are discussed.

Novel long-chain neurotoxins from Bungarus candidus distinguish the two binding sites in muscle-type nicotinic acetylcholine receptors

αδ-Bungarotoxins, a novel group of long-chain α-neurotoxins, manifest different affinity to two agonist/competitive antagonist binding sites of muscle-type nicotinic acetylcholine receptors (nAChRs), being more active at the interface of α-δ subunits. Three isoforms (αδ-BgTx-1-3) were identified in Malayan Krait (Bungarus candidus) from Thailand by genomic DNA analysis; two of them (αδ-BgTx-1 and 2) were isolated from its venom. The toxins comprise 73 amino acid residues and 5 disulfide bridges, being homologous to α-bungarotoxin (α-BgTx), a classical blocker of muscle-type and neuronal α7, α8, and α9α10 nAChRs. The toxicity of αδ-BgTx-1 (LD₅₀ = 0.17-0.28 µg/g mouse, i.p. injection) is essentially as high as that of α-BgTx. In the chick biventer cervicis nerve-muscle preparation, αδ-BgTx-1 completely abolished acetylcholine response, but in contrast with the block by α-BgTx, acetylcholine response was fully reversible by washing. αδ-BgTxs, similar to α-BgTx, bind with high affinity to α7 and muscle-type nAChRs. However, the major difference of αδ-BgTxs from α-BgTx and other naturally occurring α-neurotoxins is that αδ-BgTxs discriminate the two binding sites in the Torpedo californica and mouse muscle nAChRs showing up to two orders of magnitude higher affinity for the α-δ site as compared with α-ε or α-γ binding site interfaces. Molecular modeling and analysis of the literature provided possible explanations for these differences in binding mode; one of the probable reasons being the lower content of positively charged residues in αδ-BgTxs. Thus, αδ-BgTxs are new tools for studies on nAChRs.

Insights into Molecular Interactions of human Wnt5b and Frizzled proteins for their role in teratogenicity

Wnt-Fzd signalling plays vital role in different physiological pathways including embryonic development and supposed to be probable target of many teratogens. The present study was done to investigate the role of human Wnt5b interaction with different isoforms of human Fzds and also the molecular interactions of their complexes with selected known teratogens [Carbamazepine (CBZ), Retinoic acid (RA), Valproic acid (VPA), Aminopterin (AMP) and Phenytoin (PHY)] using Niclosamide (NLM) as standard. The models of hWnt5b and hFzd isoforms, whose solved crystal structures were unavailable, were generated using homology modeling and hWnt5b was subjected to protein-protein docking studies against different isoforms of hFzd. The macromolecular docking studies of hWnt5b-hFzds complexes revealed that hWnt5b had highest binding affinity with hFzd8 and lowest with hFzd1, respectively. The Cysteine rich domain (CRD) of hFzds docked against hWnt5b into a palm shaped opening or near the largest binding pocket as in hWnt5b-hFzd6. The possible role of Wnt-Fzd interactions in developmental toxicity due to selected teratogens were also investigated using molecular docking studies which showed that Retinoic Acid possessed the maximum binding affinity with binding energy of for hWnt5b-hFzd8 complex while VPA was observed to have lowest binding affinity towards all the studied hWnt5b-hFzd complexes.

Docking software performance in protein-glycosaminoglycan systems

We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned. Our results suggest that Dock program performs best in terms of the pose placement, has the most suitable scoring function, and its performance did not depend on the ligand size. This suggests that the implementation of the electrostatics as well as the shape complementarity procedure in Dock are the most suitable for docking glycosaminoglycan ligands. We also analyzed how free energy patterns of the benchmarking complexes affect the performance of the evaluated docking software.

Dipeptidyl peptidase IV Inhibitory activity of Terminalia arjuna attributes to its cardioprotective effects in experimental diabetes: In silico, in vitro and in vivo analyses

BACKGROUND

The marketed synthetic (Dipeptidyl peptidase-IV) DPP-IV Inhibitors are expensive antidiabetic drugs and have been reported to cause unacceptable adverse effects such as pancreatitis, angioedema, thyroid and pancreatic cancers. In this scenario research to develop novel DPP-IV Inhibitors from alternative sources is the need of the hour.

HYPOTHESIS/PURPOSE

Terminalia arjuna, a medicinal herb with antidiabetic and cardioprotective activities may represent a natural DPP-IV Inhibitor, the DPP-IV Inhibitory activity of which may translate into demonstrable therapeutic benefits in setting of diabetes with cardiovascular co-morbidities.

STUDY DESIGN

The study type used for the present study was an experimental (In vitro, In vivo and In silico) design.

METHOD

The DPP-IV Inhibitory, antidiabetic and cardioprotective effects of Terminalia arjuna was evaluated in the experimental model of myocardial infarction co-existing with diabetes. To determine the active principle of Terminalia arjuna responsible for DPP-IV Inhibitory activity, the crystal structure of DPP-IV was considered as receptor which was docked against Arjunetin, Arjungenin, Arjunic acid, Arjunone, Ellagic acid, Gallic acid, Sitagliptin and Vildagliptin. The binding sites as well as affinity of various active ingredients of Terminalia arjuna for DPP- IV enzyme was elucidated using in silico studies and compared to Vildagliptin.

RESULTS

Terminalia arjuna demonstrated significant DPP-IV Inhibitory, antidiabetic (significant reduction in HbA_1C) and cardioprotective effects (restoration of myocardial CPK-MB) in the experimental model of myocardial infarction co-existing with diabetes. The cardioprotective efficacy correlated to its DPP-IV Inhibitory activity. The active ingredients of Terminalia arjuna (Arjunetin, Arjungenin, Arjunic Acid Arjunone, Ellagic acid and Gallic acid) demonstrated significant inhibition of DPP-IV enzyme. Arjunic acid and Arjunone prefers the active site pocket of DPP-IV enzyme. Compounds like Arjunetin and Vildagliptin prefers to bind near the interface region of the DPP-IV as their biological active forms are homodimer. Sitagliptin binds near the α/β hydrolase domain.

CONCLUSION

The DPP-IV Inhibitory activity of Terminalia arjuna was found to be comparable to Vildagliptin. The DPP-IV Inhibitory activity translated into significant cardioprotective effects in the setting of diabetes. The active ingredient of Terminalia arjuna; Arjunetin, Arjungenin, Ellagic acid and Arjunic acid showed superior DPP-IV Inhibitory activity as compared to synthetic DPP-IV inhibitors (Sitagliptin and Vildagliptin) based on results of docking studies.

Engineering of the upper hinge region of human IgG1 Fc enhances the binding affinity to FcγIIIa (CD16a) receptor isoform

The interaction between antibodies and Immune cells surface FcγRIIIa (CD16a) receptor triggers a variety of immune responses including antibody-dependent cell-mediated cytotoxicity, antibody neutralization, phagocytosis, inflammation and tissue injury. Recent studies showed that IgG1 upper hinge region and FcγRs polymorphism play a major role in the interaction with Fcγ receptors and in the stability of the immune complex hence, in mounting strong inflammatory response. To further investigate this issue, we developed a tool box of IgG1 Fc isoforms to depict the affinity between mutated IgG1 Fc regions and extracellular domain variants (V158F) of CD16a. Our strategy consisted of designing different random upper-hinge mutated variants of IgG1 Fc domain, reproducing the naturally occurring two variants of CD16a and producing all of them as recombinant fusion proteins in Pichia Pastoris. The interactions were assayed using the Surface Plasmon Resonance (Biacore) method along with an in silico analysis to identify the major interaction and key residues that underline the affinity between the Fc region and CD16a variants. Our data showed that the affinity of the Fc region to the CD16a is strongly correlated to polar interactions. This molecular engineering approach yielded an IgG1Fc mutant with enhanced binding affinity to CD16a F158 variant.

Benchmarking of different molecular docking methods for protein-peptide docking

Background

Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There are several benchmarking studies on protein-protein, protein-ligand and nucleic acid-ligand docking interactions. However, a series of docking methods is not rigorously validated for protein-peptide complexes in the literature. Considering the importance and wide application of peptide docking, we describe benchmarking of 6 docking methods on 133 protein-peptide complexes having peptide length between 9 to 15 residues. The performance of docking methods was evaluated using CAPRI parameters like FNAT, I-RMSD, L-RMSD.

Result

Firstly, we performed blind docking and evaluate the performance of the top docking pose of each method. It was observed that FRODOCK performed better than other methods with average L-RMSD of 12.46 Å. The performance of all methods improved significantly for their best docking pose and achieved highest average L-RMSD of 3.72 Å in case of FRODOCK. Similarly, we performed re-docking and evaluated the performance of the top and best docking pose of each method. We achieved the best performance in case of ZDOCK with average L-RMSD 8.60 Å and 2.88 Å for the top and best docking pose respectively. Methods were also evaluated on 40 protein-peptide complexes used in the previous benchmarking study, where peptide have length up to 5 residues. In case of best docking pose, we achieved the highest average L-RMSD of 4.45 Å and 2.09 Å for the blind docking using FRODOCK and re-docking using AutoDock Vina respectively.

Conclusion

The study shows that FRODOCK performed best in case of blind docking and ZDOCK in case of re-docking. There is a need to improve the ranking of docking pose generated by different methods, as the present ranking scheme is not satisfactory. To facilitate the scientific community for calculating CAPRI parameters between native and docked complexes, we developed a web-based service named PPDbench (http://webs.iiitd.edu.in/raghava/ppdbench/).

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2449-y) contains supplementary material, which is available to authorized users.

Structural insights into pro-aggregation effects of C. elegans CRAM-1 and its human ortholog SERF2

Toxic protein aggregates are key features of progressive neurodegenerative diseases. In addition to “seed” proteins diagnostic for each neuropathy (e.g., Aβ_1–42 and tau in Alzheimer’s disease), aggregates contain numerous other proteins, many of which are common to aggregates from diverse diseases. We reported that CRAM-1, discovered in insoluble aggregates of C. elegans expressing Q40::YFP, blocks proteasomal degradation of ubiquitinated proteins and thus promotes aggregation. We now show that CRAM-1 contains three α-helical segments forming a UBA-like domain, structurally similar to those of mammalian adaptor proteins (e.g. RAD23, SQSTM1/p62) that shuttle ubiquitinated cargos to proteasomes or autophagosomes for degradation. Molecular modeling indicates that CRAM-1, through this UBA-like domain, can form tight complexes with mono- and di-ubiquitin and may thus prevent tagged proteins from interacting with adaptor/shuttle proteins required for degradation. A human ortholog of CRAM-1, SERF2 (also largely disordered), promotes aggregation in SH-SY5Y-APP_Sw human neuroblastoma cells, since SERF2 knockdown protects these cells from amyloid formation. Atomistic molecular-dynamic simulations predict spontaneous unfolding of SERF2, and computational large-scale protein-protein interactions predict its stable binding to ubiquitins. SERF2 is also predicted to bind to most proteins screened at random, although with lower average stability than to ubiquitins, suggesting roles in aggregation initiation and/or progression.

d-Amino Acid Pseudopeptides as Potential Amyloid-Beta Aggregation Inhibitors

A causative factor for neurotoxicity associated with Alzheimer's disease is the aggregation of the amyloid-β (Aβ) peptide into soluble oligomers. Two all d-amino acid pseudo-peptides, SGB1 and SGD1, were designed to stop the aggregation. Molecular dynamics (MD) simulations have been carried out to study the interaction of the pseudo-peptides with both Aβ13⁻23 (the core recognition site of Aβ) and full-length Aβ1⁻42. Umbrella sampling MD calculations have been used to estimate the free energy of binding, ∆G, of these peptides to Aβ13⁻23. The highest ∆Gbinding is found for SGB1. Each of the pseudo-peptides was also docked to Aβ1⁻42 and subjected up to seven microseconds of all atom molecular dynamics simulations. The resulting structures lend insight into how the dynamics of Aβ1⁻42 are altered by complexation with the pseudo-peptides and confirmed that SGB1 may be a better candidate for developing into a drug to prevent Alzheimer's disease.

Design of peptide epitope from the neuraminidase protein of influenza A and influenza B towards short peptide vaccine development

Influenza viruses A and B are important human respiratory pathogens causing seasonal, endemic and pandemic infections in several parts of the globe with high morbidity and considerable mortality. The current inactivated and live attenuated vaccines are not effective. Therefore, it is of interest to design universal influenza virus vaccines with high efficacy. The peptide GQSVVSVKLAGNSSL of pandemic influenza, the peptide DKTSVTLAGNSSLCS of seasonal influenza and the peptide DILLKFSPTEITAPT of influenza B were identified as potential linear cell mediated epitopes. The epitopes predicted by BepiPred (B-cell epitope designer) program was subjected to docking experiment-using HexDock and CABS dock programs. The epitopes of pandemic H1N1 influenza A gave similar score of high affinity in docking. The epitope DKTSVTLAGNSSLCS of seasonal influenza A and epitope DILLKFSPTEITAPT of influenza B had high binding energy. It is further observed that the peptides GQSVVSVKLAGNSSL (pandemic influenza), DKTSVTLAGNSSLCS (seasonal influenza) DILLKFSPTEITAPT (influenza B) are found to interact with some known MHC class II alleles. These peptides have high-affinity binding with known MHC class II alleles. Thus, they have the potential to elicit cell immune response. These vaccines have to be further evaluated in animal models and human volunteers. These findings have application in the development of peptide B-cell epitope vaccines against influenza viruses.

A novel peptide ligand RAP12 of LRP1 for glioma targeted drug delivery

The receptor associated protein (RAP) is a 39 kDa chaperone protein, binding tightly to low-density lipoprotein receptor-related protein-1 (LRP1) that is overexpressed in glioma, tumor neovasculature, vasculogenic mimicry (VM), the blood-brain barrier (BBB) and the blood-brain tumor barrier (BBTB). Herein, we miniaturized the RAP protein into a short peptide RAP12 (EAKIEKHNHYQK) aiding by computer-aided peptide design technique. RAP12 contained the essential lysines at the positions 253 and 256. The binding affinity of RAP12 to LRP1 was theoretically and experimentally evaluated. In cellular level, RAP12 could effectively internalize into U87, HUVEC and bEnd.3 cells. When modified on the surface of PEG-PLA micelles (RAP12-PEG-PLA), RAP12 could effectively facilitate the penetration of micelles through the BBB/BBTB in vitro/vivo. Paclitaxel-loaded RAP12-PEG-PLA could remarkably inhibit the growth of glioma cells and the formation of tumor neovasculature and VM, significantly prolong the median survival time of nude mice bearing intracranial glioma in comparison to model mice treated with plain micelles or Taxol. These results suggested that the RAP12 held the potential for multifunctional glioma-targeted drug delivery.

β- N-Methylamino-l-alanine (BMAA) Not Involved in Alzheimer's Disease

β- N-Methylamino-l-alanine (BMAA) is a neurotoxic agent implicated in ALS as well as Parkinson's and Alzheimer's diseases. It is produced by blue-green algae and could find its way via fish and seafood into the human food supply. Isolation from biological samples yields the compound in monomeric and protein-bound form. It has been suggested that the protein-bound fraction may result from genetic misincorporation into proteins in place of serine. Concomitant misfolding of the mutated proteins may be responsible for the neurological diseases. Recent reports that contradict the misincorporation theory leave unresolved the nature of the protein-bound form of BMAA. We have found from quantum mechanical calculations on model systems that it is possible to bind BMAA with high affinity in a noncovalent fashion to proteins. Because of our interest in Alzheimer's disease, molecular dynamics simulations were applied to search for such binding between BMAA and the β-amyloid peptide and to discover whether replacement of either of its two serine residues could affect its aggregation into neurotoxic oligomers. No stable noncovalently bound complex was found, and it was concluded that incorporation of BMAA in place of serine would not alter the conformational dynamics of the β-amyloid peptide.

Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking

Ab initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 19 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or void-volume distance. For most test cases, the rank of the top-scoring near-native prediction was improved by at least twofold compared with docking without the cross-link information, and the success rate for the top 5 predictions nearly tripled. Our results demonstrate the delicate balance between retaining correct predictions and eliminating false positives. Several test cases had multiple components with distinct interfaces, and we present an approach for assigning cross-links to the interfaces. Employing the symmetry information for these cases further improved the performance of complex structure prediction.

Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor

The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF₁R and CRF₂R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF₂R in addictive-related neuronal plasticity and behavior. In addition, it has been described that CRF-BP is capable to physically interact specifically with the α isoform of CRF₂R and acts like an escort protein increasing the amount of the receptor in the plasma membrane. At present, there are no available structures for CRF-BP or for full-length CRFR. Knowing and studying the structure of these proteins could be beneficial in order to characterize the CRF-BP/CRF_2αR interaction. In this work, we report the modeling of CRF-BP and of full-length CRF_2αR and CRF_2βR based on the recently solved crystal structures of the transmembrane domains of the human glucagon receptor and human CRF₁R, in addition with the resolved N-terminal extracellular domain of CRFRs. These models were further studied using molecular dynamics simulations and protein-protein docking. The results predicted a higher possibility of interaction of CRF-BP with CRF_2αR than CRF_2βR and yielded the possible residues conforming the interacting interface. Thus, the present study provides a framework for further investigation of the CRF-BP/CRF_2αR interaction.

In silico validation of microalgal metabolites against Diabetes mellitus

Aim. Present study aimed to evaluate the efficiency of microalgal metabolites as ligands for anti-diabetic target proteins viz., glucokinase, fructose-1, 6-bisphosphatase, glycogen synthase kinase, cytochrome P450, multi drug resistant protein, and peroxisome proliferator-activated receptor-(PPAR) via computational approach. Matherials and methods. Three-dimensional structures of microalgal metabolites were retrieved from PubChem database and were energy minimized. The active site of target protein was predicted through PDB sum. Molecular docking was performed with microalgae metabolites by using Hex 8.0 and DockThor server. Results. Hex docking revealed that the binding interaction of fucoxanthin was higher with fructose 1.6 bis-phosphatase (-298.31), human multidrug resistant protein 1 (-369.67), and PPAR(-404.18). DockThor docking indicated that zeaxanthin with glucokinase produced higher total energy (111.23 kcal/mol) and interaction energy (-2.99 kcal/mol). Lutein with fructose 1.6 bis phosphatase, human multidrug resistant protein, glycogen synthase kinase, PPARand cytochrome p450 produced higher total energy and interaction energy. Conclusion. Further studies will assess the anti-diabetic effect of carotenoids of microalgae especially lutein, zeaxanthin and fucoxanthin.

Computational insights into promoter architecture of toxin-antitoxin systems of Mycobacterium tuberculosis

Toxin-antitoxin (TA) systems are two component genetic modules widespread in many bacterial genomes, including Mycobacterium tuberculosis (Mtb). The TA systems play a significant role in biofilm formation, antibiotic tolerance and persistence of pathogen inside the host cells. Deciphering regulatory motifs of Mtb TA systems is the first essential step to understand their transcriptional regulation. In this study, in silico approaches, that is, the knowledge based motif discovery and de novo motif discovery were used to identify the regulatory motifs of 79 Mtb TA systems. The knowledge based motif discovery approach was used to design a Perl based bio-tool Mtb-sig-miner available at (https://github.com/zoozeal/Mtb-sig-miner), which could successfully detect sigma (σ) factor specific regulatory motifs in the promoter region of Mtb TA modules. The manual curation of Mtb-sig-miner output hits revealed that the majority of them possessed σ^B regulatory motif in their promoter region. On the other hand, de novo approach resulted in the identification of a novel conserved motif [(T/A)(G/T)NTA(G/C)(C/A)AT(C/A)] within the promoter region of 14 Mtb TA systems. The identified conserved motif was also validated for its activity as conserved core region of operator sequence of corresponding TA system by molecular docking studies. The strong binding of respective antitoxin/toxin with the identified novel conserved motif reflected the validation of identified motif as the core region of operator sequence of respective TA systems. These findings provide computational insight to understand the transcriptional regulation of Mtb TA systems.

Pseudo-peptide amyloid-β blocking inhibitors: molecular dynamics and single molecule force spectroscopy study

By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-β (Aβ) inhibitors that bind to the Aβ peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aβ (13-23). The binding affinities between the inhibitor and Aβ as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aβ-Aβ binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aβ toxicity in Alzheimer's disease.